The standard format for The Comedy Channel's shows usually involved the various hosts introducing clips culled from the acts of stand-up comedians as well as classic comedies of the 1970s and 1980s, such as Young Frankenstein and Kentucky Fried Movie, presented in a style similar to music videos. In the early days, certain hours of the day when clips were shown without "host segments" were dubbed Short Attention Span Theater. In 1990, hosts under this title, Jon Stewart and Patty Rosborough, were introduced. Comedian Marc Maron also hosted the series.

While The Comedy Channel broadcast mostly low-budget original programming,[6] Ha!'s schedule featured sitcom and sketch comedy reruns (many of which had been previously licensed for sister network Nick at Nite) as well as complete 90-minute reruns of Saturday Night Live from the sixth through 16th seasons.

After two years of limited distribution, the two channels merged into one, relaunching on April 1, 1991 as CTV: The Comedy Network; it later changed its name to Comedy Central on June 1, 1991 to prevent issues with the Canadian broadcast television network CTV.[7] Viacom bought out Time Warner's half in April 2003 for $1.23 billion.[8] Despite HBO's exit from the venture, the Viacom Media Networks division in charge of Comedy Central is still called Comedy Partners, currently being a partnership of Viacom International, the operating subsidiary of Viacom of which Viacom Media Networks is a division, and Viacom Hearty Ha! Ha! LLC, the subsidiary that owned Ha! and Viacom's original half of the network.[9]

The original Comedy Central logo used from 1991-2000. An earlier variant of this logo has the "Comedy Central" text bigger, almost taking up the marquee sign; that variant lasted until 1995.

From the late 1980s through the mid-1990s, much of the programming on Comedy Central and its predecessors consisted of comedy films, sitcom reruns, half-hour specials, and clip shows featuring comedians. With the exception of the cult favorite Mystery Science Theater 3000, the channel had a relatively small viewership. A notable early success was Politically Incorrect with Bill Maher, which after showing promise on Comedy Central was quickly snapped up by ABC. Additionally, The Daily Show had got its start with original host Craig Kilborn, although it would take a few more years for the show to reach high popularity (and a shift toward a focus on political humor) with the introduction of Jon Stewart (who was former co-host of Short Attention Span Theater from 1991).

Dr. Katz, Professional Therapist was also a notable original program from this era, as well as the game show Win Ben Stein's Money. Successful non-original programming included Canadian comedy group The Kids in the Hall and British shows such as the U.K. edition of Whose Line Is It Anyway? (the predecessor of the U.S. version, featuring much of the same American cast as would later be seen in the U.S.) and the sitcom Absolutely Fabulous. Some later seasons of "AbFab", as it was informally known, were partially financed by Comedy Central. Comedy Central also had the national rights to broadcast reruns of Seattle's Almost Live! between 1992 and 1993.

The channel made a breakthrough when South Park premiered in 1997. Being the first major basic cable show to carry the TV-MA rating for mature audiences, the show was too controversial to be picked up by a mainstream network.[10] As word of mouth spread, the number of people who requested that Comedy Central be added to their cable providers increased, and the channel became available in over 50% of American homes by 1998.

The network's second logo used from 2000-2010. It was used in the United Kingdom until 2012.

In October 2000, Comedy Central modernized its globe logo, by straightening the buildings and removing the transmitter. The management of the network said that the transmitter of the 1991 logo was said to "communicate the 1950s broadcast era". In 2002, Comedy Central Records was formed as a means of releasing albums by comedians that have appeared on the network.[11]

The success of South Park, despite its mature content, encouraged the network to continue to push the limits on adult language. Every Saturday and Sunday morning at 1 a.m. ET, a movie, comedy special, or animated program is shown unedited for language as part of a block called the Secret Stash. It premiered on July 4, 2003 with the unedited cable television debut of South Park: Bigger, Longer & Uncut. Though no language is censored on the Secret Stash, most nudity in the programs is still edited out, with the exception of limited nudity allowed in animated programs such as Drawn Together, and rear nudity.

In late 2004, it was reported that the four highest-rated shows on Comedy Central were, in descending order, South Park, Chappelle's Show, The Daily Show and Reno 911!. Shortly thereafter, Dave Chappelle backed out of the much-anticipated third season of Chappelle's Show.[20] Meanwhile, The Daily Show continued to climb in the ratings. In October 2005, on the occasion of a new three-year contract for South Park and the launch of Daily Show spin-off The Colbert Report, it was reported that South Park and The Daily Show were the two highest-rated shows on Comedy Central. Comedy Central chief Doug Herzog was reported as saying that he hoped to continue to air new seasons of South Park forever, and that The Colbert Report fulfilled a long-held plan to extend the Daily Show brand.

On April 5, 2006, in a controversial two-part episode arc titled "Cartoon Wars Part I" and "Cartoon Wars Part II", South Park touched the issue of the recent protest over the Danish cartoon drawings depicting the Muslim prophet Muhammad. The image of Muhammad did not appear in the episode. The episode also mocked fellow cartoon Family Guy. On April 13, 2006, Comedy Central issued a statement[21] which appears to confirm that the network prohibited the show's creators from airing an image of Muhammad. The statement reads, "In light of recent world events, we feel we made the right decision." An anonymous source close to the show indicated[citation needed] that South Park creators Trey Parker and Matt Stone were informed of the policy several weeks earlier, and wrote this story arc in protest. This was a change of policy for Comedy Central, having allowed South Park to portray an image of Muhammad in an earlier episode, "Super Best Friends". Oddly enough, an image of Muhammad was still briefly visible in the opening credits of the "Cartoon Wars" episodes (the image had been there as a call-back to "Super Best Friends").

On January 15, 2007, MTV Networks International launched Comedy Central in Germany which is available for free throughout Europe. The channel airs 33 shows either dubbed in German or subtitled while also airing locally produced shows.[22] On April 30, Dutch channel The Box was relaunched as the Dutch version of Comedy Central during the primetime and overnight hours timesharing with Nickelodeon.[23] On May 1, 2007, Comedy Central expanded to Italy, replacing Paramount Comedy.[24]

On June 27, 2007, CTVglobemedia-owned networks CTV and The Comedy Network obtained the exclusive Canadian rights to the entire Comedy Central library of past and current programs on all electronic platforms, under a multi-year agreement with Viacom, expanding on past programming agreements between the two channels. Canadian users attempting to visit Comedy Central websites were redirected to The Comedy Network's website. The Canadian channel retains its own brand name, but the agreement is otherwise very similar to the earlier CTV/Viacom deal for MTV in Canada.[25] As of 2011, this geocaching no longer applies and both the Comedy Central and The Comedy Network websites can be accessed worldwide, with the exception of videos which remain only accessible within each respective country.

In December 2007, Comedy Central picked up a show hosted by Lewis Black called Lewis Black's Root of All Evil,[26] which debuted in March 2008. On January 9, 2008, it was announced the Comedy Central and MTV would allow the streaming its programs online for free starting in February of that year.[27] On January 24, Scott Landsman became the Vice President of Original Programming and Development at the network.[28]

On March 27, 2008, the Swedish Radio and TV Authority approved an application from Comedy Central regarding being allowed to air television programs in Sweden. The grant allows Comedy Central to broadcast on the terrestrial television network between January 1, 2009 and March 31, 2014, after which a new request must be submitted in order to continue broadcasting.[29] Comedy Central's U.S. flagship network picked up a remake of The Gong Show hosted by Dave Attell,[30] star of his former self-titled Comedy Central series Insomniac, which debuted in July 2008. Another new show called Reality Bites Back[31] premiered after The Gong Show with Dave Attell.

In June 2008, Comedy Central picked up the sketch comedy show Important Things with Demetri Martin, which began airing in February 2009.[32] On April 1, 2009, Comedy Central began airing in New Zealand as channel 010 on SKY Digital. On April 6, Paramount Comedy in the UK and Ireland rebranded as Comedy Central. On April 7, 2009, it was announced Comedy Central would air new stand-up comedy specials starring Christopher Titus, Gabriel Iglesias, Pablo Francisco, Jim Breuer, Mitch Fatel and Pete Correale, and ventriloquist Jeff Dunham.[33] An animated show entitled Ugly Americans was also picked up by the network.[34] In 2009, The Goode Family premiered.[35] Also in 2009, Thomas Lennon announced via Twitter that Reno 911! had been cancelled[36] after six seasons, much to fan disapproval. The network also played a role in the revival of the animated series Futurama, which Fox had cancelled in 2003. New episodes began airing on Comedy Central in 2010. But in May 2013, Comedy Central released a statement saying that the contract between Futurama and Comedy Central would not be renewed, and that the summer of 2013 would be Futurama's final season on the air. However, episodes continue to run daily on Comedy Central.[37]

South Park episodes "200" and "201" aired in April 2010, revisiting the issue of the Islamic religious figure Muhammad's perceived immunity to parody, for fear of violent retaliation. The Super Best Friends returned, but Muhammad was entirely covered by a black bar reading "CENSORED" through all of his screen time. By the second episode of the two-parter, Comedy Central decided to censor every instance of his name, as well as three entire monologues, from the end of the show. The monologues dealt with the subjects of censorship and intimidation, but did not actually use Muhammad's name. Parker and Stone have since issued a statement to the press, confirming that the "bleeps" were added weeks after the show was finished, and that Comedy Central has refused to let them post the original version to South Park Studios, in addition to retroactively removing the original "Super Best Friends" episode.[38]

On December 10, 2010, Comedy Central introduced a new logo for the network that launched on January 1, 2011, which left behind the previous theme of a world-sized "tower" broadcasting the network/skyscrapers, in favor of an image of two "C"'s, with one of them and the word "Central" turned upside-down within the new logomark. The new logo was designed to represent the network's unique brand of comedy (with some drawing comparisons to the copyright symbol as inspiration for its design and use), and to provide the network with a logo that could be easily used across different platforms, such as social media.[39][40] The logo's resemblance to the one used by Federal Communications Commission has also been pointed out.[41][42] It went on to win several industry awards.[43] The company also standardised its publicity material and idents to use the fonts Brandon Grotesque and Eames Century Modern.[44]

The Polish version of the channel was the first international Comedy Central channel to switch to the new logo on February 20, 2011; followed by the Hungarian version on April 1, 2011. Versions of the channel in Germany and the Netherlands soon followed on October 1, 2011. Comedy Central New Zealand rebranded in April 2012. Viacom 18 launched the channel in India on January 23, 2012.[45]StarHub launched Comedy Central Asia in Singapore on November 1, 2012; the channel was added to its Basic Entertainment Upsize group.[46]

In 2014 it was announced that Stephen Colbert would leave Comedy Central to host Late Show with Stephen Colbert on CBS, following the retirement of David Letterman, the first host of Late Show. The final episode of The Colbert Report aired on Comedy Central on December 18, 2014, after nine years and a total of 1,447 episodes. The final episode of The Colbert Report was watched by 2.481 million viewers, making it the most watched episode ever in the show's history. The finale was the most watched cable program of the night in its time slot, beating The Daily Show which was seen by 2.032 million viewers.[48][49]The Colbert Report was replaced on Comedy Central by Larry Wilmore from The Daily Show, who began hosting his series The Nightly Show with Larry Wilmore on January 19, 2015.[50]

On February 10, 2015 Jon Stewart announced that he would retire from hosting The Daily Show, after 16 years of hosting. Stewart's final show would be on August 6, 2015. From September 28, 2015 onwards, Trevor Noah would take Stewart's duties.[51]